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Peak Picking and Fitting

Peak Picking and Fitting

Peak pick selected area

To pick the peaks in a particular area, hold down Shift and Ctrl (Cmd on a Mac) while left-dragging the mouse. A blue box will be drawn and peaks will be picked at all visible extrema (maxima and minima) in that area. If you find you are picking too many or too few peaks, adjust your contour levels and remember to show/hide positive/negative contours depending on which you would like to have picked. For more information on adjusting contour levels, go to Customise Spectrum Display.

Alternatively you can type PP or go to Spectrum / Pick Peaks / Pick ND Peaks.... A pop-up will appear in which you can select the area in which you would like to pick peaks (by default the whole spectrum area is included). Choose whether to pick positive or negative peaks or both and click on Find Peaks to pick your peaks. You can also choose whether to estimate linewidths or calculate volumes at the same time as picking your peaks (see Peak fitting and volumes below).

Manual peak pick (peak placing)

Press Shift and Ctrl/Cmd while left-clicking the mouse where you would like to place your peak.

Alternatively you can type MM and the mouse will go into peak picking mode. You can now easily place multiple peaks in various places in quick succession. Type MM again to exit the peak picking mouse mode.

If you would like to snap any manually placed peaks to their closest extremum (maximum or minimum), simply select them and type SE.

Peak picking in 3D spectra

This is the same as peak picking in 2D spectra, but be aware that if you are not in the plane containing the maximum or minimum of your peak, Shift + Ctrl/Cmd + left-dragging to pick a peak may not work. Move planes until you think you are near the maximum and try again, or place a peak manually and type SE. Navigate to the correct plane to find the peak on the peak extremum, or use the shortcut FP to find/navigate to the peak.

It is also possible to peak pick a 3D spectrum based on its 2D root spectrum. You can do this either using the Pick and Assign function or within AnalysisStructure by going to Structure / Restricted Peak Pick.

Peak fitting and volumes

When you pick peaks either with Shift+Ctrl/Cmd+drag or the PP pop-up, the program will do a quick analytical (parabolic) fit which will give you an estimation of the peak line widths. This keeps the peak picking process fast. A better fit (which may take a minute or two when you execute it on 100s or 1000s of peaks in one go) can be done by selecting peaks and using RP to refit your peaks. If you have any overlapping peaks, then you can select those separately and use RG to refit a group of peaks which will usually give you a better fit. You can check the quality of the fit by changing your peak symbols to filled line widths (e.g. by cycling the peak symbols with PS: the filled blob should fit nicely onto your peak if the fit is good.

If you wish to calculate your peak volumes (e.g. using Spectrum / Estimate Peak Volumes... or shortcut EV) you will first need to have line widths associated with your peak, i.e. you will have to have picked your peaks with Shift+Ctrl/Cmd+drag or the PP pop-up (possibly followed by using RP) or you need to use RP on any manually placed peaks. You can always check in your Peak List table whether your peaks have line widths or volumes associated with them.

Peak picking parameters

In your Preferences (go to File / Preferences or type Ctrl/Cmd + ,) in the Peaks tab you will find a section on Peak Picking. The 1d Peak Picking Drop and nD Peak Picking Drop parameters specify the percentage by which a peak must drop off from its maximum in all directions (or rise from its minimum) in order to be recognised as a peak. The higher this value, the less likely you are to pick partially overlapped peaks or peaks with shoulders on them. Note that while our default nD Peak Picker uses this parameter, the 1d peak picker does not. By default, the 1d Peak picker will not pick negative peaks. Select Include negative peaks 1D if you would like to pick negative 1D peaks.

In the Peak Fitting section you can select to add a refit (RP) after a snap-to-extremum (SE) automatically every time. The Peak Interpolation Method (options are parabolic or gaussian) refers to the fitting method used when refitting with RG.